Review of Basic Phylogenetic Combinatorics by Andreas Dress, Katharina T. Huber, Jacobus Koolen, Vincent Moulton, Andreas Spillner Cambridge University Press, 2012

摘要

Phylogenetics is the science of relationships between organisms, as measured by some characteristic, such as gene, genome, RNA or protein sequence (the authors of the present work abstract slightly and refer to the concept of an Operational Taxonomic Unit, or OTU). A frequent object of study in phylogenetics is to ascertain the nature and order of the evolution of a group of OTUs, such as a set of animal species - which species are closely related, and which diverged in evolution less recently? Additionally, phylogenetic analysis can have more practical applications and has been used in the study of viruses and other pathogens as well. Generally the OTU or characteristic of interest in a phylogenetic analysis is sequence based: gene and genome sequences, composed of nucleotides, are represented as strings over the alphabet {A, C, G, T}, (or similar for RNA) and protein sequences, composed of amino acids, as strings over all English letters except {B, J, O, U, X, Z}. In such a phylogenetic analysis, the question of similarity is specified to be about similarity of sequence and the series of changes needed to get from one sequence to another. This is a difficult problem, because methods for phylogenetics must account for different factors, including site-specific (individual nucleotide or amino acid position) and general mutation rates.